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Tom Paris, the inventor, barrels through Fair Haven on an automobile, wreaking havoc until a pile of barrels stops him. He explains that he fell into some money with inheritance. He tells the computer to repair a damaged tire, which appears. When Seamus sees that happen, he comes to a very simple conclusion: it is black magic.

He goes to the pub, and uses the money Paris gave him to wash down his troubles. He tells everyone what he saw; "Tommy boy" make a new wheel appear in thin air, and he is going to Castle O'Dell, which is haunted with evil spirits, later. He goes through town as if he built the place, and his friends are shifty.

Soon, legends start coming out about towns where spirit folk sneaked in, took advantage of their hospitality, and took all the people to the other world. The entire town vanished.

Meanwhile, on the rest of the ship, Harry Kim replicates flowers for someone, a lovely Irish lass named Maggie O'Halloran. B'Elanna Torres complains about her technical difficulties with the program when Paris decides to make Kim's date a little more interesting.

As he starts looking for Kim, Seamus and Milo follow him around, determined to prove he is a demon. As Kim talks about his ship to Maggie, a sailing ship, and the moment comes when he gets to hold her hand and kiss her, Paris reprograms Maggie into a cow. They are ordered to the bridge soon after, and Seamus sees the whole thing with Milo. They are flabbergasted.

That night, Father Mulligan gives a sermon about harmony, and the evils of retribution. When he begins to get to his climax, Seamus and Milo enter with the cow which used to be Maggie. They point out that it was the trickery of Paris and Kim. The Doctor reassures them that it was just a prank, and he saw Maggie this morning. He kicks them out.

They do find Maggie outside, who appears just before they get there. She doesn't seem herself, as she had a dream without remembering going to sleep. She doesn't remember anything about last night, but remembers walking around town with a bell around her neck, showing up at church, and everyone staring at her. She was tending her flowers just as they walked up.

They return to the bar, and more people start telling stories, of how Kim and Paris can change the weather, a daughter who fell in a well reappearing in the meadows, and Father Mulligan disappearing after service one night. Sullivan puts a stop to it, saying that there is nothing they can do; they can't just shoot everyone they suspect, since they are their neighbors. He wants them to go about the situation like civilized people.

Later, when Sullivan is alone with Katie O'Clare, he hands her a copy of The Faerie Queene, suggesting that the townsfolk are wondering about strange things happening. He even did some checking, and there is no one who knows her (supposed) point of origin. He wants to know where she goes when she leaves and more about her to put his thoughts at ease. She admits she hasn't been honest, but not about anything important. She tries to explain that there are things he just cannot understand, but he wants to know. She doesn't know what to say, so she ends the program.

Janeway demands to know what Paris did with the program. He says nothing he did should result in that. Torres shuts the program down so she can make system repairs, and Paris and Kim begin to examine the character parameters. When they call up Michael Sullivan's character, instead of his image, the entire character comes to life, now in the hololab and sees them wearing their uniforms. He demands to know where he is, but they calm him down. They identify the subroutines which make him oblivious to things outside the program, and those subroutines are offline. They attempt to restore them, and as he realizes something is off-kilter, he pretends to appear to think nothing is out of the ordinary instantly (as the subroutines still don't go into effect). But when they find a way to restore all of the other characters at once, it is clear from his facial expression – which they miss – he was pretending to be complacent. The stunned, almost angry, Michael Sullivan calls Fitzgerald into the church.

Only later do Paris and Kim figure out they failed, and plan to reset him along with everyone else. Janeway argues with Chakotay about what to do if they can't fix Michael. He suggests she get creative.

Sullivan, meanwhile, tells Fitzgerald an incredible story: he was taken to another world, and they were saying things about changing people and talking like he wasn't even there. They decide to be prepared for whatever will happen at the Pub that night (the way to reset all of their programs using one of the hubs inside the building). While Kim and Paris sneak into the pub to do it, the town gathers to discuss strategy. Some want to use rifles, some want to use books, some want to use rowan berries and red thread. Sullivan doesn't like it, but he is drowned out by Seamus. They head right over to the pub, and catch them in a red thread net, and when they see the control panel, they shoot it repeatedly to dispel the voice from the other world complaining about the failure of the safety protocols. When Paris orders the computer to freeze the program, half the characters freeze, and the other half chase them. When Paris and Kim can't pause the program or call up an exit, they capture them and hold them in the church.

In the ready room, the rest of the senior staff discuss what to do. Transporters can't get a lock, they don't want to shut down the program or they'll lose it, and armed conflict would risk the lives of their security personnel. Instead, Janeway decides to send in The Doctor who can attach pattern enhancers to Paris and Kim to retrieve them.

Meanwhile, the exorcisms of Paris and Kim, tied up with red twine and having incantations shouted, isn't going very well. When they are discussing lynching, The Doctor bursts in and condemns them all as 'sinners'. They ignore him, pointing out he vanished after his sermon, and tie him up with the others. They take away the transport enhancers, and The Doctor's mobile emitter, tying him into the same grid.

They learn from The Doctor, under hypnosis, that there is a ship called Voyager. Sullivan believes Katie is there and he asks The Doctor how to get there, having come back once before. The Doctor suggests the mobile emitter, and when Tuvok beams it to the bridge without looking, Janeway is astonished to see Sullivan materialize. He is more astonished than she is. She is forced to explain everything as feels she has no choice. She explains that Voyager is a time ship, like H.G. Wells, and that many members of the crew he recognizes just visit Fair Haven because they are explorers.

As Sullivan begins to understand, and slowly come to terms with the starship, Tuvok announces through the comm that the townspeople have started piling kindling. She returns to the holodeck program with Sullivan, and she explains to the townspeople that they use technology, not magic, and they do not wish to destroy their town. In fact, Sullivan points out that they helped the town by creating clear days and saving children (turning Maggie into a cow excepted, which Paris promises not to do again). Sullivan convinces them not to turn their backs on these people, and everyone cools down.

Torres once again complains about the limits of holographic technology, saying they will have to limit the time the program runs. Janeway regretfully accepts this fact, but with her last short time in the program, finds that everything is back to normal, with holographic and flesh and blood characters, more or less.

In this episode, Tom Paris says, "So much for my open-door policy." However, it was actually Neelix who suggested the "open door protocol" to Captain Janeway in the episode "Fair Haven".

Also in "Fair Haven", when discussing the rewriting of the program, Paris and Janeway say it will take six or seven weeks to complete. The two episodes are six apart numerically and were originally aired six weeks apart.

In the final dialogue of the episode, Sullivan tells Janeway that knowing a spirit's true name renders one impervious to their charms, but Janeway insists that she doesn't believe a word of it. In "Fair Haven", she restricts herself access to his matrix, so he is, in effect, impervious to her charms.